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<pre>
/////////////////////////////////////////////////////////////////////////////////////
// //
// INDELible V1.03 control file - trees.txt //
// //
// How to define user trees and how to generate random trees... //
// //
/////////////////////////////////////////////////////////////////////////////////////
<font color=red>[TYPE] NUCLEOTIDE 1</font> // nucleotide simulation using algorithm from method 1
<font color=red>[MODEL] mymodel [submodel] JC </font>
// You will have already come across user-defined trees in the other examples.
// The following three trees are identical - "white space" of any kind is ignored.
<font color=red>[TREE] t1 ((A:0.1,B:0.1):0.1,(C:0.1,D:0.1):0.1);</font>
<font color=red>[TREE] t2 ( (A:0.1, B:0.1):0.1, (C:0.1, D:0.1):0.1 );</font>
<font color=red>[TREE] t3 </font>
<font color=red> ( </font> // trees can span any number of lines
<font color=red> ( </font> // and include any amount of whitespace
<font color=red> A:0.1, </font> // including new lines.
<font color=red> B:0.1 </font>
<font color=red> ):0.1 , </font> // comments within the tree will be ignored.
<font color=red> (C:0.1,D:0.1):0.1); </font>
// But any tree can also be rescaled to be a certain tree length.
// For example the two following trees are identical.
<font color=red>
[TREE] T1 ((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);
[treelength] 4.2
[TREE] T2 ((A:0.2,B:0.4):0.6,(C:0.8,D:1.0):1.2);
</font>
// Random rooted & unrooted trees can also be created by INDELible.
// A different tree will be generated for each replicate.
// Explanation of these commands follow the examples...
<font color=red>
[TREE] tree1
[unrooted] 10 2.4 1.1 0.2566 0.34 </font>// ntaxa birth death sample mut
<font color=red>
[TREE] tree2
[unrooted] 10 2.4 1.1 0.2566 0.34 </font>// ntaxa birth death sample mut
<font color=red>[seed] 2381242 </font>
<font color=red>
[TREE] tree3
[rooted] 15 6.7 2.5 0.234 0.31 </font>// ntaxa birth death sample mut
<font color=red>[treedepth] 0.4</font></font>
<font color=red>
[TREE] tree4
[rooted] 15 6.7 2.5 0.234 0.31 </font>// ntaxa birth death sample mut
<font color=red>[treelength] 8</font></font>
/*
* Random trees always have taxa names that are numbers.
e.g. (1:0.1,2:0.1,(3:0.1,4:0.1):0.1);
* <font color=blue>tree1</font> and <font color=blue>tree2</font> will be unrooted random trees.
* <font color=blue>tree3</font> and <font color=blue>tree4</font> will be rooted random trees.
* Every time that INDELible is run <font color=blue>tree2</font> will produce the same sequence
of random trees, until the number after the <font color=blue>[seed]</font> command is changed.
* The others (<font color=blue>tree1</font>, <font color=blue>tree3</font> and <font color=blue>tree4</font>) will always produce different trees.
* Please note that the <font color=blue>[seed]</font> command overrules the <font color=blue>[randomseed]</font>
command from a <font color=blue>[SETTINGS]</font> block, for a random tree.
* <font color=blue>tree4</font> will produce random trees that are always rescaled to have a tree
length of 8, and <font color=blue>tree3</font> will produce random trees that are always rescaled
to have a depth (root to tip) of 0.4, whilst the other two (<font color=blue>tree1</font> and
<font color=blue>tree2</font>) will always produce random trees with different tree lengths/depths.
* The numbers that come after the <font color=blue>[unrooted]</font> and <font color=blue>[rooted]</font> commands are
the same in both cases. The first number is the number of taxa
(10 for tree1 and tree2, 15 for tree3 and tree4).
* The next four are the parameters used in the birth-death process to
create the random trees. In order, from left to right, these are the
<font color=blue>birth-rate</font>, <font color=blue>death-rate</font>, <font color=blue>sampling fraction</font> and <font color=blue>mutation rate</font>.
Further details on these parameters can be found in this paper:
<a href="http://abacus.gene.ucl.ac.uk/ziheng/pdf/1997YangRannalaMBEv14p717.pdf" target="_blank">http://abacus.gene.ucl.ac.uk/ziheng/pdf/1997YangRannalaMBEv14p717.pdf</a>
* Trees (random or user) that are used during the simulation will be output
by INDELible in a file <a href="trees.txt" target="_blank">like this</a>.
* One last point to remember about random trees is that they CANNOT be
used when you want the evolutionary model to be permitted to change
over the tree. i.e. they CANNOT be used with [BRANCHES] blocks.
*/
// For a given topology INDELible can also create branch lengths.
// This is done by using the command [branchlengths]
// Further explanation of the four examples is given below
<font color=red>
<a name="branchlengths"></a>
[TREE] EQUAL-TREE
</font> // No branch lengths need to be provided<font color=red>
((((A,B),(C,D)),((E,F),(G,H))),(((I,J),(K,L)),((M,N),(O,P))));
[branchlengths] EQUAL </font>// All branch lengths will be equal
<font color=red>[treedepth] 0.1</font> // Root-to-longest-tip distance of 0.1
<font color=red>
[TREE] EQUAL-TREE2
</font> // If branch lengths are provided, they are ignored<font color=red>
((((A:0.2,B:0.1):0.4,(C:0.3,D:0.1):0.6):0.1,
((E:0.1,F:0.1):0.1,(G:0.2,H:0.1):0.1):0.3):0.1,
(((I:0.1,J:0.6):0.1,(K:0.1,L:0.1):0.1):0.1,
((M:0.4,N:0.1):0.1,(O:0.6,P:0.1):0.1):0.1):0.1);
[branchlengths] EQUAL </font>// Again, all branch lengths will be equal
<font color=red>[treedepth] 0.1</font> // Root-to-longest-tip distance of 0.1
<font color=red>
[TREE] ULTRAMETRIC-TREE
</font> // No branch lengths need to be provided<font color=red>
((((A,B),(C,D)),((E,F),(G,H))),(((I,J),(K,L)),((M,N),(O,P))));
[branchlengths] ULTRAMETRIC </font>// All branch lengths will be equal
<font color=red>[treedepth] 0.1</font> // Root-to-longest-tip distance of 0.1
<font color=red>
[TREE] NON-ULTRAMETRIC-TREE
</font> // No branch lengths need to be provided<font color=red>
((((A,B),(C,D)),((E,F),(G,H))),(((I,J),(K,L)),((M,N),(O,P))));
[branchlengths] NON-ULTRAMETRIC </font>// All branch lengths will be equal
<font color=red>[maxdistance] 0.2</font> // Maximum pairwise distance of 0.2
/*
* <font color=blue>[treedepth] 0.1</font> rescales the tree to have a maximum root-to-tip distance of 0.1
* After using the <font color=blue>[branchlengths]</font> command you should use <font color=blue>[treelength]</font> or
<font color=blue>[treedepth]</font>, or <font color=blue>[maxdistance]</font> to rescale your tree.
* <font color=blue>[branchlengths] EQUAL</font> will make every branch on the tree equal to 0.1.
* <font color=blue>[branchlengths] NON-ULTRAMETRIC</font> gives every branch a random length between 0 and 1.
* <font color=blue>[branchlengths] ULTRAMETRIC</font> gives every branch a random length between 0 and 1,
but will also extend the terminal branches so that the root-to-tip distance is
the same for every tip.
* If the <font color=blue>[branchlengths]</font> command is used then the tree toplogy can be specified
with or without branch lengths. It does not matter. Any branch lengths will be ignored.
i.e. the trees EQUAL-TREE and EQUAL-TREE2 will be identical.
* Examples of the trees produced above can be seen <a href="random_branch_length_trees.JPG">here</a>.
* All trees in the image are rescaled to have a maximum tree-depth of 0.1.
This means that the root-to-tip distance for taxon G is equal to 0.1 in all 3 trees.
* N.B. For ultrametric trees <font color=blue>[maxdistance] 0.2</font> is equivalent to <font color=blue>[treedepth] 0.1</font>
For the non-ultrametric tree they are not the same.
<font color=blue>[maxdistance] 0.2</font> on the non-ultrametric tree scales the tree such that the sum of
the branch lengths in between (in <a href="random_branch_length_trees.JPG">this</a> case) taxons G and N would be 0.2
*/
<font color=red>[PARTITIONS] Pname1 [t1 mymodel 1000]</font> // tree t1, model mymodel, root length 1000
<font color=red>[PARTITIONS] Pname2 [t2 mymodel 1000]</font> // tree t2, model mymodel, root length 1000
<font color=red>[PARTITIONS] Pname3 [t3 mymodel 1000]</font> // tree t3, model mymodel, root length 1000
<font color=red>[PARTITIONS] Pname4 [T1 mymodel 1000]</font> // tree T1, model mymodel, root length 1000
<font color=red>[PARTITIONS] Pname5 [T2 mymodel 1000]</font> // tree T2, model mymodel, root length 1000
<font color=red>[EVOLVE] Pname1 10 outputname1</font> // 10 replicates generated from partition Pname1
<font color=red> Pname2 10 outputname2</font> // 10 replicates generated from partition Pname2
<font color=red> Pname3 10 outputname3</font> // 10 replicates generated from partition Pname3
<font color=red> Pname4 10 outputname4</font> // 10 replicates generated from partition Pname4
<font color=red> Pname5 10 outputname5</font> // 10 replicates generated from partition Pname5
</pre>
<br><hr><br>
Please click <a href="http://abacus.gene.ucl.ac.uk/software/indelible/tutorial/">here</a> to return to the tutorial menu page for more examples.
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